7P1Z | pdb_00007p1z

Novel GH12 endogluconase from Aspergillus cervinus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5GM3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		288	Peg 6000 18,5% 0.2M CaCl2 0.1M NaAcetate pH 5.0

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.094	α = 90
b = 118.364	β = 90
c = 125.702	γ = 90

Symmetry
Space Group	P 2 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2019-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	0.8	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.17	125.7	99.6	0.152	0.18	0.095	0.995	7.8	6.5		37115

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.17	2.24			0.715	0.862	0.475	0.866		6.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5GM3	2.17	62.93	37069	1893	99.389	0.186	0.1835	0.18	0.2305	0.23	30.421

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
7.06			-3.219		-3.841

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.605
r_dihedral_angle_4_deg	28.415
r_dihedral_angle_3_deg	11.755
r_dihedral_angle_1_deg	7.511
r_lrange_it	5.785
r_scangle_it	3.921
r_mcangle_it	3.48
r_scbond_it	3.175
r_mcbond_it	2.471
r_angle_refined_deg	1.413
r_metal_ion_refined	0.53
r_nbtor_refined	0.316
r_symmetry_nbd_refined	0.286
r_nbd_refined	0.217
r_xyhbond_nbd_refined	0.137
r_symmetry_xyhbond_nbd_refined	0.135
r_chiral_restr	0.098
r_ncsr_local_group_1	0.074
r_ncsr_local_group_2	0.07
r_ncsr_local_group_3	0.051
r_bond_refined_d	0.008
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5120
Nucleic Acid Atoms
Solvent Atoms	358
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
DIALS	data reduction
PHASER	phasing